Fourth Army commander Lt Gen Udomchai Thammasaroraj has set up a panel to investigate whether two commissioned officers were involved in the alleged trafficking of Rohingya migrants.
The officers hold the rank of major and lieutenant, an army source said.
They are attached to the Internal Security Operations Command's (Isoc) 4th Region Forward Command.
Army chief Gen Prayuth Chan-ocha instructed Lt Gen Udomchai to set up the probe after police and NGO officials told him the pair were involved in trafficking the migrants, the source said.
''If any officers are guilty of trafficking, the Fourth Region Army will not protect them,'' Lt Gen Udomchai said.
Foreign Ministry spokesman Manasvi Srisodapol urged the international community to join Thailand in seeking a solution for the Rohingya migrants who have fled Myanmar and who are now being held in the South.
Mr Manasvi said the migrants left Myanmar via Thailand for a third country and do not want to return home. He said Thailand is holding talks with other countries to solve the problem.
The ministry is also talking to international organisations such as the United Nations High Commissioner for Refugees (UNHCR), Mr Manasvi said.
''The government is serious about tackling human trafficking and the Rohingya migrant problem has affected Thailand in the eyes of the international community,'' he said.
Thailand is now providing the Rohingya migrants with temporary assistance on a humanitarian basis.
It is sheltering 949 Rohingya migrants, most of whom were picked up in raids in the South earlier this month.
Most are in Songkhla and the rest have been sent to Narathiwat, Trang, Pattani and Phangnga provinces.
In Songkhla, the UNHCR and Foreign Ministry officials yesterday visited 105 Rohingya children and women at a shelter run by the Ministry of Social Development and Human Security, as well as Rohingya men at other shelters in the province.
Meanwhile, Col Narin Pannarai, deputy director of the Isoc in Ranong, dismissed reports that a shelter for the Rohingya migrants would be set up in the province. ''Ranong province does not have the facilities to take care of these migrants because officials are having to deal with problems of Myanmar, Cambodian and Lao workers in the province,'' he said.
Marine police yesterday inspected a boat floating in the sea near Phangnga and found 179 Rohingya migrants, after being informed of the boat's presence.
Pol Lt Col Laksanawong Rampansuwan, deputy chief of marine police at Phangnga's Khura Buri district, said they found the 179 Rohingya migrants crammed into the boat.
The migrants had spent 16 days travelling from Myanmar's Rakhine state, and many more are expected to arrive in Thailand soon.
The Rohingya migrants, all of them men, are being sheltered at Khura Buri police station.